[gmx-users] T-coupling of water and ion

[Anton Feenstra]

Jian Zou wrote:
> I just generate 8 ADE, dissolve it in a water box, run EM, PR, then MD.
> Therefore, the starting structure is taken from the PR-MD result.

And which ref_t did you use during PR-MD?

> This sounds reasonable to me.
> But I'm still wondering why couple Na seperately will give the 
> temperature for RNA 100 degree C lower than the ref_t.

Your *whole* system is (far) below the 400K ref_t. I can't see how your 
.mdp file could have produced these results. Are you sure these are the 
settings you used? Perhaps you can check your .tpr file or md.log (or 
md0.log)?


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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